Why do the Boolean options disappear when the Boolean modifier is applied?
The idea is that you don't apply a modifier until you need to (if at all). It is not uncommon to never apply the modifiers if you don't need to directly access their result in edit mode. You can leave modifiers in the modifier 'stack', which allows you to turn them on or off, re-order them and change their settings. Once you apply the modifier, any changes the modifier makes are written directly (and permanently) to the mesh.

As you say, the only way to undo the effects after applying a modifier is to undo, restore a previous version of the file (if you have one) or restore a previous version of the mesh (if you have one).

Because applying a modifier is 'destructive' (to the original object) it is not uncommon to either not apply the modifiers or to keep a copy of the original mesh on a spare layer if they do need to be applied.